<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<!-- DTD for polymer definitions, used by the
'massXpert' mass spectrometry application.
Copyright 2006,2007,2008 Filippo Rusconi
Licensed under the GNU GPL -->
<!DOCTYPE polchemdefinition [
<!ELEMENT polchemdefinition (polchemdefdata)>
<!ATTLIST polchemdefinition version NMTOKEN #REQUIRED>
<!ELEMENT polchemdefdata (name , leftcap , rightcap , codelen , ionizerule , monomers , modifs , crosslinkers , cleavageagents , fragmentationpathways)>
<!ELEMENT ionizerule (formula , charge , level)>
<!ELEMENT monomers (mnm*)>
<!ELEMENT modifs (mdf*)>
<!ELEMENT crosslinkers (clk*)>
<!ELEMENT cleavageagents (cla*)>
<!ELEMENT fragmentationpathways (fgp*)>
<!ELEMENT mnm (name , code , formula)>
<!ELEMENT mdf (name , formula , targets , maxcount)>
<!ELEMENT clk (name , formula , modifname*)>
<!ELEMENT cla (name , pattern , clr*)>
<!ELEMENT fgp (name , end , formula , sidechaincontrib , comment? , fgr*)>
<!ELEMENT clr (name , (le-mnm-code , le-formula)? , (re-mnm-code , re-formula)?)>
<!ELEMENT fgr (name , formula , prev-mnm-code? , curr-mnm-code? , next-mnm-code? , comment?)>
<!ELEMENT leftcap (#PCDATA)>
<!ELEMENT rightcap (#PCDATA)>
<!ELEMENT codelen (#PCDATA)>
<!ELEMENT charge (#PCDATA)>
<!ELEMENT maxcount (#PCDATA)>
<!ELEMENT level (#PCDATA)>
<!ELEMENT name (#PCDATA)>
<!ELEMENT modifname (#PCDATA)>
<!ELEMENT code (#PCDATA)>
<!ELEMENT formula (#PCDATA)>
<!ELEMENT sidechaincontrib (#PCDATA)>
<!ELEMENT targets (#PCDATA)>
<!ELEMENT pattern (#PCDATA)>
<!ELEMENT end (#PCDATA)>
<!ELEMENT le-mnm-code (#PCDATA)>
<!ELEMENT re-mnm-code (#PCDATA)>
<!ELEMENT le-formula (#PCDATA)>
<!ELEMENT re-formula (#PCDATA)>
<!ELEMENT comment (#PCDATA)>
<!ELEMENT prev-mnm-code (#PCDATA)>
<!ELEMENT curr-mnm-code (#PCDATA)>
<!ELEMENT next-mnm-code (#PCDATA)>
]>
<polchemdefinition version="2">
	<polchemdefdata>
		<name>protein-1-letter-c-n-full-heavy</name>
		<leftcap>"N-term amine" +H</leftcap>
		<rightcap>"C-term carboxylic acid" +OH</rightcap>
		<codelen>1</codelen>
		<ionizerule>
			<formula>+H</formula>
			<charge>1</charge>
			<level>1</level>
		</ionizerule>
		<monomers>
			<mnm>
				<name>Glycine</name>
				<code>G</code>
				<formula>C2H3N1O1</formula>
			</mnm>
			<mnm>
				<name>Alanine</name>
				<code>A</code>
				<formula>C3H5N1O1</formula>
			</mnm>
			<mnm>
				<name>Valine</name>
				<code>V</code>
				<formula>C5H9N1O1</formula>
			</mnm>
			<mnm>
				<name>Leucine</name>
				<code>L</code>
				<formula>C6H11N1O1</formula>
			</mnm>
			<mnm>
				<name>DiaminoPimelic</name>
				<code>O</code>
				<formula>C7H12N2O3</formula>
			</mnm>
			<mnm>
				<name>Isoleucine</name>
				<code>I</code>
				<formula>C6H11N1O1</formula>
			</mnm>
			<mnm>
				<name>Serine</name>
				<code>S</code>
				<formula>C3H5N1O2</formula>
			</mnm>
			<mnm>
				<name>Threonine</name>
				<code>T</code>
				<formula>C4H7N1O2</formula>
			</mnm>
			<mnm>
				<name>Cysteine</name>
				<code>C</code>
				<formula>C3H5N1O1S1</formula>
			</mnm>
			<mnm>
				<name>Methionine</name>
				<code>M</code>
				<formula>C5H9N1O1S1</formula>
			</mnm>
			<mnm>
				<name>Arginine</name>
				<code>R</code>
				<formula>C6H12N4O1</formula>
			</mnm>
			<mnm>
				<name>Lysine</name>
				<code>K</code>
				<formula>C6H12N2O1</formula>
			</mnm>
			<mnm>
				<name>Aspartate</name>
				<code>D</code>
				<formula>C4H5N1O3</formula>
			</mnm>
			<mnm>
				<name>Glutamate</name>
				<code>E</code>
				<formula>C5H7N1O3</formula>
			</mnm>
			<mnm>
				<name>Asparagine</name>
				<code>N</code>
				<formula>C4H6N2O2</formula>
			</mnm>
			<mnm>
				<name>Glutamine</name>
				<code>Q</code>
				<formula>C5H8N2O2</formula>
			</mnm>
			<mnm>
				<name>Tryptophan</name>
				<code>W</code>
				<formula>C11H10N2O1</formula>
			</mnm>
			<mnm>
				<name>Phenylalanine</name>
				<code>F</code>
				<formula>C9H9N1O1</formula>
			</mnm>
			<mnm>
				<name>Tyrosine</name>
				<code>Y</code>
				<formula>C9H9N1O2</formula>
			</mnm>
			<mnm>
				<name>Histidine</name>
				<code>H</code>
				<formula>C6H7N3O1</formula>
			</mnm>
			<mnm>
				<name>Proline</name>
				<code>P</code>
				<formula>C5H7N1O1</formula>
			</mnm>
		</monomers>
		<modifs>
			<mdf>
				<name>Acetylation</name>
				<formula>C2H2O1</formula>
				<targets>;K;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>AmidationAsp</name>
				<formula>H1N1-O1</formula>
				<targets>;D;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>AmidationGlu</name>
				<formula>H1N1-O1</formula>
				<targets>;E;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Carbamidomethylation</name>
				<formula>C2H3N1O1</formula>
				<targets>;C;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Carbamylation</name>
				<formula>C1H1N1O1</formula>
				<targets>;K;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>CarboxyMethylation</name>
				<formula>C2H2O2</formula>
				<targets>;C;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Chromo-O</name>
				<formula>-O1</formula>
				<targets>;T;S;G;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Chromo-H</name>
				<formula>-H1</formula>
				<targets>;G;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Chromo-H3</name>
				<formula>-H3</formula>
				<targets>;Y;F;W;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Dehydroalanine</name>
				<formula>-H2S1</formula>
				<targets>;C;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>DTNB (adsorbed)</name>
				<formula>C14H8N2O8S2</formula>
				<targets>;C;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Dehydroxylation</name>
				<formula>-H1O1</formula>
				<targets>;D;E;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Formylation</name>
				<formula>C1O1</formula>
				<targets>*</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>GlcNAcMurNAc(R)</name>
				<formula>C19H32N2O12</formula>
				<targets>*</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Glutamylation</name>
				<formula>C5H7N1O3</formula>
				<targets>;E;</targets>
				<maxcount>6</maxcount>
			</mdf>
			<mdf>
				<name>Glycylation</name>
				<formula>C2H3N1O1</formula>
				<targets>;E;</targets>
				<maxcount>34</maxcount>
			</mdf>
			<mdf>
				<name>Hydroxylation</name>
				<formula>H1O1</formula>
				<targets>;F;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>LysMethylation</name>
				<formula>C1H2</formula>
				<targets>;K;</targets>
				<maxcount>3</maxcount>
			</mdf>
			<mdf>
				<name>Methylation</name>
				<formula>C1H2</formula>
				<targets>;K;R;</targets>
				<maxcount>2</maxcount>
			</mdf>
			<mdf>
				<name>Oxidation</name>
				<formula>O1</formula>
				<targets>;M;Y;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Phosphorylation</name>
				<formula>H1O3P1</formula>
				<targets>;S;T;Y;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>ProtonLoss</name>
				<formula>-H1</formula>
				<targets>;C;Y;K;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Pyroglutamylation</name>
				<formula>-NH3</formula>
				<targets>;E;Q;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>SulfideBond</name>
				<formula>-H2</formula>
				<targets>;C;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>Sulphation</name>
				<formula>O3S1</formula>
				<targets>;S;T;Y;</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>SPITC</name>
				<formula>C7H5N1O3S2</formula>
				<targets>*</targets>
				<maxcount>1</maxcount>
			</mdf>
			<mdf>
				<name>TNB</name>
				<formula>C7H3N1O4S1</formula>
				<targets>;C;</targets>
				<maxcount>1</maxcount>
			</mdf>
		</modifs>
		<crosslinkers>
   <clk>
    <name>GFP-chromophore</name>
    <formula>-H+H</formula>
    <modifname>Chromo-O</modifname>
    <modifname>Chromo-H3</modifname>
    <modifname>Chromo-H</modifname>
   </clk>
			<clk>
				<name>CFP-chromophore</name>
				<formula/>
				<modifname>Chromo-O</modifname>
				<modifname>Chromo-H3</modifname>
				<modifname>Chromo-H</modifname>
			</clk>
			<clk>
				<name>DisulfideBond</name>
				<formula/>
				<modifname>ProtonLoss</modifname>
				<modifname>ProtonLoss</modifname>
			</clk>
		</crosslinkers>
		<cleavageagents>
			<cla>
				<name>Chymotrypsin</name>
				<pattern>W/;V/</pattern>
			</cla>
			<cla>
				<name>CyanogenBromide</name>
				<pattern>M/</pattern>
				<clr>
					<name>Homoseryl</name>
					<re-mnm-code>M</re-mnm-code>
					<re-formula>-CH2S+O</re-formula>
				</clr>
			</cla>
			<cla>
				<name>EndoAspN</name>
				<pattern>/D</pattern>
			</cla>
			<cla>
				<name>EndoAspN+GluN</name>
				<pattern>/D;/E</pattern>
			</cla>
			<cla>
				<name>EndoAspN-Trypsin</name>
				<pattern>/D;K/;R/;-K/P</pattern>
			</cla>
			<cla>
				<name>EndoLysC</name>
				<pattern>K/</pattern>
			</cla>
			<cla>
				<name>GluC</name>
				<pattern>E/</pattern>
			</cla>
			<cla>
				<name>Trypsin</name>
				<pattern>K/;R/;-K/P</pattern>
			</cla>
		</cleavageagents>
		<fragmentationpathways>
			<fgp>
				<name>a</name>
				<end>LE</end>
				<formula>-C1O1H1</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
			<fgp>
				<name>b</name>
				<end>LE</end>
				<formula>-H</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
			<fgp>
				<name>c</name>
				<end>LE</end>
				<formula>+N1H2</formula>
				<sidechaincontrib>0</sidechaincontrib>
				<comment>that's just a comment</comment>
			</fgp>
			<fgp>
				<name>imm</name>
				<end>NE</end>
				<formula>-C1O1</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
			<fgp>
				<name>x</name>
				<end>RE</end>
				<formula>+C1O1-H1</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
			<fgp>
				<name>y</name>
				<end>RE</end>
				<formula>+H1</formula>
				<sidechaincontrib>0</sidechaincontrib>
			</fgp>
			<fgp>
				<name>z</name>
				<end>RE</end>
				<formula>-N1H1</formula>
				<sidechaincontrib>0</sidechaincontrib>
				<comment>Typically in ECD of protonated ions</comment>
			</fgp>
		</fragmentationpathways>
	</polchemdefdata>
</polchemdefinition>
